Method for synthesizing selectively labeled rna

ABSTRACT

The invention relates to a method for synthesizing a selectively labeled RNA, and an apparatus for performing the method. Specific segments or discrete residues within the RNA may be selectively labeled, and different segments may include different labels.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. patent application Ser. No.14/903,738, filed Jan. 8, 2016 which is a national phase applicationunder 35 U.S.C. § 371 of International Application No.PCT/US2014/045784, filed Jul. 8, 2014 which claims priority to U.S.Provisional Application Ser. No. 61/843,864 filed Jul. 8, 2013, each ofwhich is incorporated here by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to a method for synthesizing a selectivelylabeled RNA and an apparatus for performing the method.

BACKGROUND OF THE INVENTION

There are mainly two methods for generating RNA molecules. They are 1)solution-phase based in vitro transcription using T7 phage RNApolymerase (hereafter referred as solution-based T7 transcription), and2) solid-phase based chemical synthesis from phosphoramidites using asynthesizer. Solution-based T7 transcription has widely been used togenerate transcript RNAs as large as several kilobases in largequantity, but is not applicable for generating specifically labeledRNAs. Chemical synthesis is used to obtain small RNAs (up to 40-60 baseslong) in minute quantity, limited by an intrinsically low coupling ratecompared to the DNA counterpart. It is possible to use the chemicalsynthesis method to generate selective labeled small RNAs, provided thatall labeling reagents are commercially available. But specificallylabeling sizable RNAs using the chemical synthesis is not practical, duean extremely low efficiency and prohibitively high cost.

Selective labeling of specific residue(s) and/or specific region(s) ofRNAs (SLOR) is now possible due to the development of the SLORtechnology. The same type of labeling has not yet become practical evenfor DNA and proteins. Provided herein is a hybrid solid-liquid phaseenzymatic method that allows specific labeling at designated residue(s)and/or segment(s) of an RNA. Selected residues can be specificallylabeled with stable isotopes such as ¹³C/¹⁵N, or with fluorophores suchas Cy3 and Cy5 rCTP, rUTP, or rNTP derivatives. The efficiency of themethod is similar to that using the solution-phase T7 transcription.

SUMMARY OF THE INVENTION

Provided herein is a method for synthesizing a RNA, which may compriseperforming an initiation stage, an elongation stage, and a terminationstage. The initiation stage may comprise (i) providing a solid phasecomprising a DNA template, wherein the DNA is attached to a solidsubstrate; (ii) providing a first liquid phase comprising a RNApolymerase and ribonucleoside triphosphates (rNTPs); (iii) mixing thesolid phase and first liquid phase; (iv) incubating the solid phase andfirst liquid phase at 4-37° C. for at least 10 minutes to initiatesynthesis of the RNA; (v) pausing the RNA synthesis by incubating thesolid phase and first liquid phase at 0-5° C. for at least 10 minutes,whereupon the solid phase comprises the RNA polymerase and the RNA beingsynthesized; and (vi) separating the solid phase from the first liquidphase.

The elongation stage may comprise (i) providing a second liquid phasecomprising rNTPs; (ii) mixing the solid phase and second liquid phase;(iii) incubating the solid phase and second liquid phase at 4-37° C. forat least 10 minutes to elongate the RNA; (iv) pausing the RNA synthesisby incubating the solid phase and second liquid phase at 0-5° C. for atleast 10 minutes; (v) separating the solid phase from the second liquidphase; and (vi) repeating steps (i)-(v) of part (b) n times, wherein nis equal to 1-100, and wherein the rNTPs in the second liquid phase arethe same or different in each repeat. The termination stage may comprise(i) providing a third liquid phase comprising rNTPs; (ii) mixing thesolid phase with the third liquid phase; (iii) incubating the solidphase and third liquid phase at 4-37° C. for at least 10 minutes; and(iv) pausing the RNA synthesis by incubating the solid phase and thirdliquid phase at at 0° C. for at least 10 minutes. The initiation,elongation, and termination stages may be repeated m times, wherein m isequal to 1-100. The rNTPs of at least one of the first liquid phase, thesecond liquid phase, or third liquid phase may comprise a label.

The DNA may have a density of 30-80% on the solid substrate, and thesolid substrate may be a bead. The bead may comprise a gel, glass, or asynthetic polymer. The bead may have a diameter of 5-100 μm. Theconcentration of DNA may be 30 μm-1 nm. The concentration of rNTP may be1-100 times the DNA concentration. The RNA polymerase may be a T7 RNApolymerase. The label may be ¹³C/¹⁵N, ²H, Cy3, Cy5, a fluorophore, aheavy atom, or a chemical modification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows an illustration of the DNA template attached to a solidsubstrate.

FIG. 2 shows an outline of the steps and cycles of a hybrid solid-liquidreaction for selectively labeling RNA. The reaction process may bedivided into three stages: initiation, elongation and termination, amongwhich elongation is further divided into multiple steps (n cycles),depending on the length of the RNA to be synthesized and the labelingscheme. The whole process can be repeated m times, depending on theamount of RNA to be synthesized and the amount of the solid-phase DNAtemplates available. This process can be carried out by hands or by anautomated RNA synthesizer.

FIG. 3 shows the secondary structure of an adenine riboswitch RNA (SEQID NO:1) (71 nt). Seven (7) site-specifically labeled riboswitch RNAsamples were synthesized by the selectively labeled RNA synthesis methoddisclosed herein (FIGS. 7-13). These are: the isotope-labeled sites ofthe three samples are nt 1-13 (FIG. 7), nt 20-26 (FIG. 8), nt 34-41(FIG. 9) and nt 48-55 (FIG. 10), respectively. Labeling at discretepositions (nt 21, 38, 39) (FIG. 11) and at a single position (nt 39)(FIG. 12) are also demonstrated. The pause positions among thetranscriptions are marked by arrows.

FIG. 4 shows an apparatus/automated platform for performing the RNAsynthesis reaction disclosed herein, which may perform a hybridsolid-liquid phase synthesis of RNA. This platform may execute reactioncycles under an inert atmosphere and desired temperatures, and may beautomatically driven by a computer program that is executed by acomputer processor.

FIG. 5 shows reaction vessels of the apparatus in FIG. 4.

FIG. 6 shows a holder for the reaction vessels in FIG. 5.

FIG. 7 shows a RNA (SEQ ID NO:1) synthesized as disclosed hereincontaining a segment selectively labeled with ¹³C/¹⁵N nucleotides atresidues 1-13, and HSQC 2D NMR spectra associated therewith.

FIG. 8 shows a RNA (SEQ ID NO:1) synthesized as disclosed hereincontaining a segment selectively labeled with ¹³C/¹⁵N nucleotides at nt20-26, and HSQC 2D NMR spectra associated therewith.

FIG. 9 shows a RNA (SEQ ID NO:1) synthesized as disclosed hereincontaining a segment selectively labeled with ¹³C/¹⁵N nucleotides at nt34-41, and HSQC 2D NMR spectra associated therewith.

FIG. 10 shows a RNA (SEQ ID NO:1) synthesized as disclosed hereincontaining a segment selectively labeled with ¹³C/¹⁵N nucleotides at nt48-55, and HSQC 2D NMR spectra associated therewith.

FIG. 11 shows a RNA (SEQ ID NO:1) synthesized as disclosed hereincontaining a segment selectively labeled with ¹³C/¹⁵N nucleotides at nt21, 38, and 39, and HSQC 2D NMR spectra associated therewith. Discreteresidues within the RNA are labeled.

FIG. 12 shows how a selectively labeled RNA at a single position (nt 39)as synthesized herein can be used to identify multiple modes of adeninebinding in a protein of interest.

FIG. 13 shows how a selectively labeled RNA as synthesized herein can beused in sFRET analysis (nt U25-Alexa 555, C68-Alexa488, C71-Biotin).

FIGS. 14A-14C illustrate a sequence of view showing the gentle stirringin reaction vessels hosted in a holder of the apparatus.

FIG. 15 shows the initiation (block 1), elongation (block 2), andtermination (block 3) steps of an exemplary RNA synthesis reaction asdescribed herein.

FIG. 16 shows the layout of the deck of an exemplary automated platformfor synthesis of a RNA as described herein.

FIG. 17 shows another view of the automated platform disclosed herein.

FIG. 18 shows another view of the automated platform disclosed herein

DETAILED DESCRIPTION

The inventors have discovered/developed a technology of synthesizing aRNA that contains selectively labeled segment(s) or discrete position(s)within the RNA. The method/technology relies on the use of a hybridsolid-liquid phase RNA polymerase transcription reaction. The RNAproducts synthesized as described herein may be critical reagents forwide applications, such as structural studies using NMR, determiningphase in X-ray crystallography, RNA-aptamer-based detection ofsubstances, bacteria or viral particles or disease diagnosis.

Surprisingly, the inventors have found that a ternary complex between asolid substrate-bound DNA template, a RNA polymerase, and a RNA beingsynthesized from the template can be stabilized so that a RNA synthesisreaction can be paused, and the solid and liquid phase can be separated.The pause can be made to occur at a particular position within the RNAbeing synthesized by controlling the mixture of NTPs within a liquidreaction mixture being added to the synthesis reaction, and by loweringthe temperature of the reaction. For example, the synthesis can bepaused just before a U that would otherwise be added to the synthesizedRNA based on the DNA template, by adding a reaction mixture containingrATP, rCTP, and rGTP, but not rUTP. Different mixtures of rNTP can beused to selectively synthesize segment(s) and/or position(s) within theRNA.

After the reaction is paused, the liquid phase containing unreactedrNTPs can be separated from the solid phase comprising the ternarycomplex, and then washed away. A liquid reaction containing a differentset of rNTPs can then be added to continue synthesizing the RNA in thenext step. During the elongation, any step can be paused, and the liquidphase washed away. The elongation step can then be continued by adding anew liquid phase containing a new mixture of rNTPs. Each liquid reactionmixture added during each segment of the elongation step can include adifferent mixture of rNTPs with different labels, so that the resultingRNA contains different segments that are labeled differently.Unexpectedly and counter-intuitively, the concentration of rNTPs used inthe RNA synthesis reactions is not in the millimolar range as istypically used in conventional in vitro transcription, but rather in themicromolar range. Accordingly, rNTPs are used at approximatelystoichiometric concentrations in comparison to the DNA template. Higherconcentrations may be inhibitory. In addition, the inventors havesurprisingly discovered that the RNA synthesis reaction must be gentlymixed so as not to produce bubbles/forms, and thus, if performed in anautomated fashion, may be slowly rotated 360°, and not mixed bystirring, shaking, or bubbling as is typically done in the art.

1. Definitions

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting. As used in thespecification and the appended claims, the singular forms “a,” “an” and“the” include plural referents unless the context clearly dictatesotherwise.

For recitation of numeric ranges herein, each intervening number therebetween with the same degree of precision is explicitly contemplated.For example, for the range of 6-9, the numbers 7 and 8 are contemplatedin addition to 6 and 9, and for the range 6.0-7.0, the numbers 6.0, 6.1,6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitlycontemplated.

rNTPs as used herein may refer to a labeled or non-labeled, derivatizedor non-derivatized, ribonucleoside triphosphate.

2. Method for Selectively Labeling RNA

Provided herein is a method for selectively labeling a RNA bysynthesizing the RNA from a DNA template using a RNA polymerase. The RNAmay be labeled within a segment, and may be labeled at a discreteposition. The method may comprise a hybrid solid-liquid phase reaction.The synthesis reaction may comprise a DNA template, which may beattached to a solid substrate, a RNA polymerase, ribonucleosidetriphosphates (rNTPs), which may be labeled and/or derivatized, Mg²⁺,dithiothreitol (DTT), a DNase inhibitor, a RNase inhibitor, and abuffer. The reaction may not include a DNase or a RNase. A liquidreaction mixture of the liquid phase may comprise NTPs, Mg²⁺, DTT, theRNase and/or DNase inhibitors, and a buffer. The method may comprise aninitiation step, an elongation step, and a termination step. One or moreof these steps may be paused by changing the temperature of thereaction, or by including a particular combination of rNTPs in thereaction. Without being bound to a particular theory, the reaction maybe paused by stabilizing a ternary complex comprising the RNApolymerase, the DNA template, and the RNA being synthesized. The pausemay be initiated by virtue of a rNTP being missing from the liquidphase, so that RNA synthesis cannot proceed past a particular positionat the DNA template. While the reaction is paused, a first liquidreaction mixture may be removed or separated from the solid phase, and asecond liquid reaction mixture may be added. The first and second liquidreaction mixtures may comprise different combinations of rNTPs, suchthat the rNTPs in the two reaction mixtures may comprise different rNTPlabels, or such that one comprises a label and the other does not. Thepaused step may be restarted by changing the reaction temperature or bychanging the combination of rNTPs in the reaction.

a. Reagents

(1) Solid Phase

The RNA synthesis reaction may comprise a solid phase, which maycomprise a DNA template attached to a solid substrate. The solidsubstrate may be a gel, glass, a polystyrene, or a synthetic polymer.The solid substrate may have a size of 5-100 μm, and may also have asize of 5-10, 5-20, 10-20, 10-50, 20-50, 20-70, 30-80, 40-100, 50-100,70-100, or 80-100 μm. The solid substrate may be a bead. During thesynthesis reaction, the solid phase may further comprise the RNApolymerase and the RNA being synthesized. The solid phase may comprise aDNase or RNase inhibitor, and may not include a DNase or RNase.

The DNA template may be attached to the solid substrate with anaffinity-based linkage, a covalent linkage, or any other linkage knownin the art. The linkage may be non-reactive, stable in the presence of areducing agent, and stable at a temperature of about 0-40° C., and mayhave a very low retention rate. The affinity-based linkage may be abiotin-avidin linkage, or any other affinity-based linkage known in theart. The avidin may be avidin, streptavidin or NEUTRAVIDIN®. TheNEUTRAVIDIN® may be a deglycosylated form of avidin from egg whites,with a mass of approximately 60,000 daltons, and from which excesscarbohydrate has been removed. The biotin may be attached to the DNAtemplate or to solid substrate, and the avidin may be attached to thesolid substrate or DNA template, respectively. The covalent linkage maybe through an amino reaction, a thiol reaction, or any other chemistryknown in the art. The covalent linkage may also be a flexible andsoluble organic chain molecule, which may be polyethylene glycol (PEG).An example of the solid substrate-DNA template linkage is shown in FIG.1.

The DNA template may have density on the solid substrate of 30-80%,30-40%, 30-50%, 40-50%, 40-60%, 50-70%, 50-80%, or 70-80%. The densitymay balance minimization of steric hindrance and maximization of thedensity of accessible templates. The DNA concentration may be 1-100,1-80, 1-50, 1-30, 5-100, 5-80, 5-50, 5-30, 5-28, 10-100, 10-80, 10-50,10-30, 20-100, 20-80, 20-50, 20-30, 40-100, 40-80, or 50-100 μM. The DNAconcentration may also be 1-10, 5-10, 5-20, 10-20, 10-50, 20-50, 20-100,or 50-100 nM, or 30 μM-1 nM.

(2) Liquid Reaction Mixture

The liquid reaction mixture may comprise a rNTP, which may be rATP,rGTP, rCTP, or rUTP. The rNTP may comprise a label, which may be aradiolabel or a fluorophore. The label may also be a heavy atom or achemical modification. The radiolabel may be deuterium, ¹³C, ¹³C/¹⁵N,²H, ³²P, ³⁵S, ⁸⁻¹⁴C, or any other label known in the art. Thefluorophore may be Cy3, Cy5, Cy5.5, fluorescein, FAM-6, DY490, DY547,DY549, DY647, DY649, DY677, Cy2, Alexa 488, Alexa 546, Alexa 555, TAMRA,WellRED D4, or WellRED D3, or any other fluorophore known in the art.The rNTP may also comprise an aminoallyl group, and may be labeled by anamine-reactive fluorescent dye, biotin, or hapten. The amino-reactivemay be Fluorophore, Methoxycoumarin, Dansyl, Pyrene, Alexa Fluor 350,AMCA, Marina Blue dye, Dapoxyl dye, Dialkylaminocoumarin, Bimane,Hydroxycoumarin, Cascade Blue dye, Pacific Orange dye, Alexa Fluor 405,Cascade Yellow dye, Pacific Blue dye, PyMPO, Alexa Fluor 430, NBD, QSY35, Fluorescein, Alexa Fluor 488, Oregon Green 488, BODIPY 493/503,Rhodamine Green dye, BODIPY FL, 2′,7′-Dichloro-fluorescein, Oregon Green514, Alexa Fluor 514, 4′,5′-Dichloro-2′,7′-dimethoxy-fluorescein (JOE),Eosin, Rhodamine 6G, BODIPY R6G, Alexa Fluor 532, BODIPY 530/550, BODIPYTMR, Alexa Fluor 555, Tetramethyl-rhodamine (TMR), Alexa Fluor 546,BODIPY 558/568, QSY 7, QSY 9, BODIPY 564/570, Lissamine rhodamine B,Rhodamine Red dye, BODIPY 576/589, Alexa Fluor 568, X-rhodamine, BODIPY581/591, BODIPY TR, Alexa Fluor 594, Texas Red dye, Naphthofluorescein,Alexa Fluor 610, BODIPY 630/650, Malachite green, Alexa Fluor 633, AlexaFluor 635, BODIPY 650/665, Alexa Fluor 647, QSY 21, Alexa Fluor 660,Alexa Fluor 680, Alexa Fluor 700, Alexa Fluor 750, or Alexa Fluor 790,or any other amine-reactive dye known in the art. The rNTP may also be arNTP derivative. The rNTP derivative may comprise a heavy atom, or anyother derivative known in the art. A rNTP herein may be incorporatedinto the RNA by SLOR. The RNA may thus be used as a RNA-based reagentfor detection and imaging. A rNTP herein may also be incorporated intothe RNA for determining phase in X-ray crystallography.

The concentration of the rNTP may be approximately stoichiometric withthe DNA concentration, and may be at a micromolar scale. The rNTPconcentration may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 9.6, 10, 96, 1-200,1-150, 1-100, 1-50, 1-10, 20-200, 20-150, 20-50 times the DNAconcentration. The rNTP may be dissolved in a buffer and may have a pHof 7.5-8.5, 7.5-8.1, 7.9-8.5, 7.9-8.2, or 8.0-8.2.

The liquid reaction mixture may comprise the RNA polymerase. The RNApolymerase, may be a T7 RNA polymerase, a T4 RNA polymerase, a T3 RNApolymerase, or a SP6 RNA polymerase. The concentration of RNA polymerasemay be about equal to or higher than the DNA concentration. The liquidreaction mixture may comprise a DNase or RNase inhibitor, and may notinclude a DNase or RNase.

The liquid reaction mixture may comprise Mg²⁺. The Mg²⁺ concentrationmay be about 1-50 mM, 10-50 mM, 10-30 mM, 20-30 mM, 20-25 mM, or 20-50mM. The DTT concentration may be about 1-10 mM, 2-10 mM, 5-10 mM, 5 mM,or 10 mM.

The liquid reaction mixture may comprise a buffer. The buffer maycomprise a Tris-saline buffer. The buffer may comprise buffer B, whichmay comprise 100 mM Tris-HCl, 100 mM K₂SO₄, 6-25 mM MgSO₄, 10 mM DTT, pH7.9. The buffer may also comprise buffer C, which may comprise 100 mMTris-HCl, 6-25 mM MgSO₄, pH 7.9. The buffer may also comprise buffer D,which may comprise 100 mM Tris-HCl, 6-25 mM MgSO₄, 10 mM DTT, pH 7.9.The liquid reaction mixture may have a pH of about 7.5-8.5, 7.5-8.1,7.9-8.5, 7.0-8.2, 7.9-8.2, or 8.0-8.2.

b. RNA Synthesis Reaction

The RNA synthesis reaction may comprise an initiation stage, anelongation stage, and a termination stage. The three stages may beperformed as cycle multiple times, and the elongation stage may beperformed multiple times within a cycle. An example of the reaction isshown in FIG. 2.

(1) Initiation Stage

The initiation stage may comprise gently mixing an initiation stagereaction mixture, which may comprise a liquid reaction mixture. Theinitiation stage reaction mixture may also comprise the RNA polymerase,rNTPs, and solid phase. The rNTPs may be not include a specific type ofrNTP, which may be rATP, rCTP, rGTP, or rUTP, such that RNA synthesiscannot proceed beyond a specific nucleotide in the DNA template byvirtue of the absence of the missing rNTP, which would otherwise beadded and allow the synthesis to continue. The initiation stage reactionmixture may be incubated at a temperature of about 0-37, 0-40, 4-40,4-37, 4-25, 5-25, 5-37, 10-40, 10-37, 10-25, or 37° C. The initiationstage reaction may be performed for about 5-30, 5-20, 5-15, 10-30,10-20, 10-15, 20-30, 10, 20, 30, 40, 50, 60 minutes, or at least 10 or60 minutes. The RNA synthesized during the initiation stage may be atleast 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20nucleotides in length, which may stabilize an initiation ternarycomplex, which may comprise the solid phase, the RNA polymerase, and theRNA being synthesized. If the RNA synthesized during the initiationstage is longer, such as at least 13, 14, or 15 nucleotides in length,the initiation ternary complex may be more stable, and the RNA synthesismore efficient.

Upon formation of an initiation ternary complex, the solid phase may beseparated from the liquid phase, and may be washed using a buffer asdisclosed herein. The washing may be performed at a temperature of about0, 1, 2, 3, 4, 5, 0-4, or 0-5° C. The solid phase may be separated fromthe liquid reaction mixture and washed several times, which may be atleast 2, 3, 4, 5 times, or 1-10, 1-20, 5-10, 5-20, or 10-20 times. Thereaction may be paused at a temperature of about 0, 1, 2, 3, 4, 5, or0-4° C. for 5-30, 5-20, 5-15, 10-30, 10-20, 10-15, 20-30, 10, 20, 30,40, 50, or 60 minutes, or at least 10 or 60 minutes, or as many as 24-48hours.

(2) Elongation Stages

The RNA synthesis reaction may comprise an elongation stage. Theelongation stage may comprise adding a liquid reaction mixture to theinitiation stage reaction mixture. The rNTPs in the liquid reactionmixture may comprise a different combination of rNTPs, or a differentset of labels, as compared to the initiation reaction mixture. Themixture of rNTPs may depend on the sequence of the DNA template, and thesegment of the RNA being synthesized that is desired to be labeled orunlabeled, as the case may be. The rNTP mixture in each liquid reactionmixture may not include a specific type of rNTP, which may be rATP,rCTP, rGTP, or rUTP, such that RNA synthesis cannot proceed beyond aspecific nucleotide in the DNA template by virtue of the absence of themissing rNTP, which would otherwise be added and allow the synthesis tocontinue. This may cause the RNA synthesis reaction to pause. The RNAsynthesis reaction may also comprise multiple elongation stages, and therNTP mixture in the liquid reaction mixture used in each elongationstage may be different, depending on the DNA template sequence and thedesired labeling for a particular segment of the RNA being synthesized.

The reaction mixture may be incubated at a temperature of about 0, 1, 2,3, 4, 0-37, 0-40, 4-40, 4-37, 4-25, 5-25, 5-37, 10-40, 10-37, 10-25, or37° C., for about 5-30, 5-20, 5-15, 10-30, 10-20, 10-15, 20-30, 10, 20,30, 40, 50, 60 minutes, or at least 10 or 60 minutes. In particular, thereaction mixture may be incubated at about 0, 1, 2, 3, 4, 5-37, 10-25 or25° C. Incubating the reaction mixture at about 0, 1, 2, 3, 4, 5, 0-4,or 0-5° C. may cause the RNA synthesis reaction to pause. The solidphase may then be separated from the liquid reaction mixture, and thesolid phase may be washed using a buffer as disclosed herein. Thewashing may be performed at a temperature of about 0, 1, 2, 3, 4, 5,0-4, or 0-5° C. The solid phase may be separated from the liquidreaction mixture and washed several times, which may be at least 2, 3,4, 5 times, or 1-10, 1-20, 5-10, 5-20, or 10-20 times. The elongationstage may be performed multiple times as desired, in order to labeldifferent segments of the synthesized RNA differently.

(3) Termination

The RNA synthesis reaction may comprise a termination stage. Thetermination stage may comprise adding a mixture of rNTPs that is missingthe rNTP that is the first nucleotide in the RNA that is synthesizedfrom the DNA template. As an example, a mixture of rATP, rCTP, and rUTP,and excluding rGTP may be added if the first residue in the RNA that issynthesized from the DNA template is a G. This may prevent re-initiationof a new round of RNA synthesis from the DNA template. The terminationstage may also comprise adding heparin, or adding rNTPs followed byincubating the reaction at about 0, 1, 2, 3, 4, 5, 0-4, or 0-5° C. Theinitiation, elongation, and termination stages may be performed multipletimes as desired, depending on the desired yield of selectively labeledRNA to be synthesized.

(4) Mixing and Separation

The reaction mixture may be gently mixed at any or all stages of the RNAsynthesis reaction, and the mixing may be performed in a reaction vessel104 (FIG. 5). The reaction vessel 104 may also be manipulated such thatthe reaction is gently mixed so that the reaction does not form bubblesor forms. For example, the reaction vessel 104 containing the reactionmay be gently rotated at certain angles so as to prevent bubbling/forms.The reaction vessel 104 may also be wobbled. The reaction vessel 104 mayalso be rotated 360 degrees at a slow rate. The reaction vessel may alsonot be stirred, shaken, or bubbled. The reaction mixture may be mixedunder an inert atmosphere at any or all stages of the RNA synthesisreaction.

The solid phase may be separated from the liquid reaction mixture by anymeans known in the art. The separation may be via centrifugation,magnetic attraction, or filtration, which may be vacuum-driven.

3. Apparatus for Selectively Labeling RNA

An apparatus, designated 100, is disclosed for selectively labeling RNA.In particular, the apparatus 100 may be an automated platform 102 thatperforms the method of RNA synthesis disclosed herein, which maycomprise performing the initiation stage, elongation stage, andtermination stage. Referring to FIGS. 4 and 5, the automated platform102 may be operatively controlled by a computer program 114 with a userinput provided by an individual. In addition, the operations of thecomputer program 114 are controlled by instructions embodied in thecomputer program 114 and executed by a computer processor 112 inoperative communication with the computer program 114.

The apparatus 100 may comprise a reaction vessel as disclosed herein.All stages of the RNA synthesis reaction may be performed in thereaction vessel 104. An example of the reaction vessel 104 is shown inFIG. 5. The reaction vessel 104 is in operative association with a motor108 that manipulates the reaction vessel 104 through a gear arrangement110 that is operatively engaged with the motor 108. In some embodiments,the motor 108 is also in operative communication with the computerprocessor 112 for controlling the manipulation of the reaction vessel104, which may be tumbled, to ensure that the reaction is not stirred,shaken or bubbled. The apparatus 100 may also comprise a holder 106 forreceiving and manipulating the reaction vessel 104 as illustrated inFIG. 6. As shown in the sequence of views in FIGS. 14A-14C, the holder106 may manipulate the reaction vessel 104 in a manner that allows agentle mixing of the reaction within the reaction vessel that does notform any bubble in the reaction. In some embodiments, the reactionvessel 104 may be rotated 360 degrees at a slow rate by the holder 106or the reaction vessel 104 may be wobbled by the holder 106. In noinstance is the reaction vessel 104 manipulated by the holder 106 suchthat the reaction vessel 104 stirs, shakes, or bubbles the reaction.FIG. 16 shows the layout of an exemplary deck of the automated platform,and FIGS. 17 and 18 show top-down views at different angles of theautomated platform.

The apparatus may comprise: an integrated gripper for transportation ofplates, solid phase extraction (SPE)-blocks, opening of a vacuum box,and inserting/extracting receiving plates or racks; stainless steel2-channel pipetting probes for delivering liquids and gases, which maybe done simultaneously, and which may have variable spacing betweenprobes (8-38 mm) for every type of probe; liquid level detection at eachprobe; precision syringe pumps for liquids (for 500 μL, 1 mL, 2.5 mL, 5mL syringes) and precision syringe pumps for gas; high speed hotplatevortexers with integrated heating to 37° C. or even higher; 110 V highspeed, low noise hotplate vortexers with integrated heating temperaturecontrol with pneumatic clamps for an external pressurized air supply(6-8 bar); one portion of a deck of the platform may be kept at 4° C.;at least one set of pressure spots for reactor/filtration vessels; awash station; a high-flow 6-way valve for six system liquids; a SPE toaccommodate the reaction/filtration vials; a holder for pressures spots,which may have at least two positions and be pneumatic; a pulse vacuumwhich may be software-controlled; positive pressure, which may besoftware-controlled, and may have two individual channels, with anexternal pressurized air supply; racks for reaction/filtration vials,and reactor filtration vessels; a work bench (may be 1200×710 mm); and awork area (which may be 1000×290 mm) with a MTP adapter.

The present invention has multiple aspects, illustrated by the followingnon-limiting examples.

Example 1 Preparation of a Partially Isotope-Labeled RNA by StepwiseTranscription

This example demonstrates the internal labeling of a 71 nucleotide-longRNA ribo-switch RNA by stepwise transcription. The stepwisetranscriptions proceed as initiation, elongation, and terminationstages. The design of stepwise transcription is flexible, and thereactions are able to be paused at certain stage and continued later,controlled by some factors, including temperature change, and rNTPadditions. The transcription system allows a reaction to be moved to theelongation stage after being paused at the initiation stage after thefirst stretch of residues for at least 24 hr at 4° C. under properbuffer conditions. This makes it possible to synthesize RNA productslabeled at different positions. Seven RNA samples that have specificsegments or residues labeled with isotope-enriched rNTPs, biotinylatedrCTP, or Alexa555 and Alexa488 rUTP derivatives have been obtained byusing the stepwise transcription method successfully.

Similar initiation stage was pursued for synthesizing the seven RNAsamples which were used in NMR or single molecule FRET studies. Miximmobilized DNA (the final concentrations of DNA vary from 5.0 μM to28.0 μM) with active T7 RNA polymerase (the concentration of T7 RNApolymerase is equal or higher than that of DNA) in buffer B (100 mMTris-HCl, 100 mM K₂SO₄, 6-25 mM MgSO₄, 10 mM DTT, pH=7.9) at atemperature between 10-37° C. The reaction containers for thetranscription reactions are 50 mL vacuum-driven filtration system(Millipore, MA). Then, incubate with rATP, rGTP, and rUTP at 37° C. (thetypes of rNTPs added are dependent on the sequence of the target RNA,and the three types of rNTPs are necessary for synthesizing the firststretch of nucleotides at the 5′-end. And the concentration ratio: rATPor rGTP:DNA=96:1, rUTP:DNA=9.6:1. The ratios among T7, rNTP and DNA aremaintained in other RNA sample synthesis, except otherwise noted in thispaper.). After 20 mins, the beads were vacuumed and rinsed by buffer C(100 mM Tris-HCl, 6-25 mM MgSO₄, pH=7.9) at least 4 times in order toremove residual rNTPs, buffer, abortive or premature RNA, free T7 RNApolymerase, and other reaction ingredient or side products that are notbound with beads. The beads should be dry after vacuum to get rid ofresidual rNTPs as much as possible, or else may cause the unwantedbypass of the later reaction steps. Procession of properly functional T7RNA polymerase was paused after synthesizing the first stretch ofresidues due to lack of rCTP after the initiation step.

In the elongation steps, buffer D (100 mM Tris-HCl, 6-25 mM MgSO₄, 10 mMDTT, pH=7.9) with different combinations of rNTPs (all 4 types of rNTPsare not present simultaneously in the reaction mixtures, exceptsometimes in the last step) are added to the beads used in initiationstep. The concentrations of the added rNTPs in the steps of elongationstage are important, and the actually added amount should be not morethan the needed amount supposedly the yield is 100% according tostoichiometry. More details for each sample preparation are described inthe following parts.

a. Labeling One Segment with ¹³C¹⁵N-rNTPs and Rest with Deuterate-rNTPs

The first 13 nucleotides at 5′-end of the 71 nt-riboswitch RNA werechosen to be ¹³C¹⁵N isotope labeled, and other residues are deuterated(RiboA-13 nt, the isotope labeled residues are shown in cyan in FIG. 7).In the initiation step, 28 μM T7 RNA polymerase were mixed with the sameamount of immobilized DNA in 15 mL transcription buffer B for 10 minutesfirstly, incubated with ¹³C¹⁵N-rATP, ¹³C¹⁵N-rGTP, and ¹³C¹⁵N-rUTP at 37°C. for 15 min with gentle rotation (concentration ratios:¹³C¹⁵N-rATP:¹³C¹⁵N-rGTP:¹³C¹⁵N-rUTP:DNA=96:96:9.6:1. In the elongationstep, added 15 mL transcription buffer D with deuterate-ATP,deuterate-CTP, deuterate-GTP, and deuterate-UTP to the beads used ininitiation step and incubated @25 C for 15 min(deuterate-ATP:deuterate-CTP:deuterate-GTP:deuterate-UTP:DNA=14:13:10:21:1).The beads were then rinsed 3 times by 15 mL buffer C, and filtratecontaining the final products was collected. In all the synthesis, thebeads were rinsed by buffer C at least 3 times after incubation withrNTPs and buffer B in step 1 or buffer D in other steps. The overallyield for synthesizing RiboA-13 nt by this method is about 30%. Thefinal products were purified by 15% denaturing PAGE before used as anNMR sample.

b. Labeling One Segment with ¹³C¹⁵N-rNTPs

(1) Six Step-Transcription to Label the L2 Loop with ¹³C¹⁵N-rNTPs (20-26Nucleotides)

Six steps were designed for preparing the NMR sample with ¹³C¹⁵N-isotopelabeled sequence shown in green in FIG. 8 (RiboA-L2). The initiationstage (step 1) is similar as described earlier, except theconcentrations of DNA and T7 RNA polymerase are both 5 μM and thereaction volume is 30 mL. In the elongation stage (step 2 to 6),different combinations of rNTPs with 30 mL buffer D were added into thebeads after the beads were rinsed 3 times by 30 mL buffer C. And therNTPs used in the elongation stage are: rATP, rCTP and rUTP in step 2(rATP:rCTP:rUTP:DNA=2:2:2:1), ¹³C¹⁵N-rATP and ¹³C¹⁵N-rGTP in step 3(¹³C¹⁵N-rATP:¹³C¹⁵N-rGTP:DNA=1:1:1), ¹³C¹⁵N-rATP and ¹³C¹⁵N-rUTP in step4 (¹³C¹⁵N-rATP:¹³C¹⁵N-rUTP:DNA=1:2:1), ¹³C¹⁵N-rGTP in step 5(¹³C¹⁵N-rGTP:DNA=2:1), and all four types of rNTPs in step 6(rATP:rCTP:rGTP:rUTP:DNA=10:11:7:17:1). And the overall yield ofproducing RiboA-L2 by using the 6 step-transcription was close to 30%.

(2) Nine Step-Transcription to Label the L3 Loop (48-54 Nucleotides)

9 steps are needed for preparing the sample RiboA-L3, in which 7nucleotides are ¹³C¹⁵N isotope labeled (shown in red in FIG. 10). Step 1was pursued as described above, and the DNA concentration is 15 μM, andthe total reaction volume is 90 mL, and the amount ratios among theadded rATP, rGTP, rUTP, and DNA are the same as previously mentioned.The next 8 steps were proceeded similarly as the elongation stepdescribed earlier except that different rNTPs with 30 mL transcriptionbuffer C were added in each step:rATP, rCTP, and rUTP in step 2(rATP:rCTP:rUTP:DNA=2:2:2:1), rATP, rGTP, and rUTP in step 3(rATP:rGTP:rUTP:DNA=3:7:8:1), rATP, rCTP, and rUTP in step 4(rATP:rCTP:rUTP:DNA=3:3:1:1), rATP and rGTP in step 5(rATP:rGTP:DNA=1:2:1), ¹³C¹⁵N-rCTP and ¹³C¹⁵N-rUTP in step 6(¹³C¹⁵N-rCTP:¹³C¹⁵N-rUTP:DNA=2:2:1), ¹³C¹⁵N-rATP in step 7(¹³C¹⁵N-rATP:DNA=3:1), rCTP, rGTP, and rUTP in step 8(rCTP:rGTP:rUTP:DNA=2:1:3:1), rATP, rCTP, and rUTP in step 9(rATP:rCTP:rUTP:DNA=2:4:5:1). The yield of the 9 step-transcription wasabout 10%.

(3) Ten Step-Transcription to Label the L1 Loop (34-42 Nucleotides)

Ten steps were necessary for synthesizing RibA-L1 (L1 loop is¹³C¹⁵N-isotope labeled, shown in blue in FIG. 9). DNA concentration usedin initiation step was 5 μM, and the total reaction volume in each stepwas 152 mL. The added rNTPs and the ratios among rNTPs and DNA arelisted as following: rATP, rGTP and rUTP(rATP:rGTP:rUTP:DNA=96:96:9.6:1) in step 1; rATP, rCTP and rUTP(rATP:rCTP:rUTP:DNA=2:2:2:1) in step 2; ATP and rGTP(rATP:rGTP:DNA=1:1:1) in step 3; rATP and rUTP (rATP:rUTP:DNA=1:2:1) instep 4; rGTP and rUTP (rGTP:rUTP:DNA=5:3:1) in step 5; rATP(rATP:DNA=1:1) in step 6; ¹³C¹⁵N-rCTP, ¹³C¹⁵N-rGTP and ¹³C¹⁵N-rUTP(¹³C¹⁵N-rCTP:¹³C¹⁵N-rGTP:¹³C¹⁵N-rUTP:DNA=1:1:4:1) in step 7; ¹³C¹⁵N-rATP(¹³C¹⁵N-rATP:DNA=1:1) in step 8; ¹³C¹⁵N-rCTP (¹³C¹⁵N-rCTP:DNA=2:1) instep 9; rATP, rCTP, rGTP and rUTP (rATP:rCTP:rGTP:rUTP:DNA=8:8:3:10:1)in step 10. The yield of synthesizing the RibA-L1 sample by 10step-transcription reactions was about 20%.

c. Labeling Two Segments with ¹³C¹⁵N-rNTPs

To label both L2 and L3 loops, the whole synthesis are divided into 12steps. In initiation step, different DNA concentration (28 μM) and thereaction volume in each step (70 mL) were used. The beads were rinsedsimilarly as described before after each step. Besides buffer B in step1 and buffer C used in step 2 to step 12, the added rNTPs and the ratiosamong rNTPs and DNA are:

rATP, rGTP and rUTP (rATP:rGTP:rUTP:DNA=96:96:9.6:1) in step 1; rATP,rCTP and rUTP (rATP:rCTP:rUTP:DNA=2:2:2:1) in step 2; ¹³C¹⁵N-rATP and¹³C¹⁵N-rGTP (¹³C¹⁵N-rATP:¹³C¹⁵N-rGTP:DNA=1:1:1) in step 3; ¹³C¹⁵N-rATPand ¹³C¹⁵N-rUTP (¹³C¹⁵N-ATP:¹³C¹⁵N-rUTP:DNA=1:2:1) in step 4;¹³C¹⁵N-rGTP (¹³C¹⁵N-rGTP:DNA=2:1) in step 5; rATP, rGTP and rUTP(rATP:rGTP:rUTP:DNA=1:4:6:1) in step 6; rATP, rCTP and rUTP(rATP:rCTP:rUTP:DNA=3:3:1:1) in step 7; rATP and rGTP(rATP:rGTP:DNA=1:2:1) in step 8; ¹³C¹⁵N-rCTP and ¹³C¹⁵N-rUTP(¹³C¹⁵N-rCTP:¹³C¹⁵N-rUTP:DNA=2:2:1) in step 9; ¹³C¹⁵N-rATP(¹³C¹⁵N-rATP:DNA=3:1) in step 10; rCTP, rGTP, and rUTP(rCTP:rGTP:rUTP:DNA=2:1:3:1) in step 11, and rATP, rCTP, and rUTP instep 12 (rATP:rCTP:rUTP:DNA=2:4:5:1). The yield of the final productafter the 11 steps was about 8%.

d. Labeling Specific Residues with Isotope-Enriched rNTPs

Four residues, ²¹A, ³⁸C and ³⁹U (FIG. 11) were the targets for testingthe capability of the step-wise transcription method in labeling singleresidues. The DNA concentration used in initiation step is 5 μM, and thetotal reaction volume was 152 mL. Eight more steps were processed, andthe added rNTPs and the ratios among rNTPs in each step are listedbelow: rATP, rGTP and rUTP (rATP:rGTP:rUTP:DNA=96:96:9.6:1) in step 1;rATP, rCTP and rUTP (rATP:rCTP:rUTP:DNA=2:2:2:1) in step 2; ¹³C¹⁵N-rATPand rGTP (¹³C¹⁵N-rATP:rGTP:DNA=1:1:1) in step 3; rATP, rGTP and rUTP(rATP:rGTP:rUTP:DNA=2:6:8:1) in step 4; ¹³C¹⁵N-rCTP and ¹³C¹⁵N-rUTP(¹³C¹⁵N-rCTP:¹³C¹⁵N-rUTP:DNA=1:1:1) in step 5; rATP, rCTP, and rGTP(rATP:rCTP:rGTP:DNA=4:4:2:1) in step 6; rATP, rCTP and rUTP(rATP:rCTP:rUTP:DNA=3:2:5:1) in step 7; ¹³C¹⁵N-rGTP(¹³C¹⁵N-rGTP:DNA=1:1) in step 8; rATP, rCTP and rUTP(rATP:rCTP:rUTP:DNA=2:4:5:1) in step 9. The yield for the synthesis wasabout 10%.

e. RNA Yields

The following table shows yields of the above-described multi-step RNAsynthesis for selectively labeling segments of RNA, as compared to RNAsynthesis from a one-step transcription based on the same DNA templateas above, either attached to a bead or free in solution.

Overall transcription yield Each step Based on template Based ontranscription yield Labeled Needed amount (before/after rATP Based onBased on Based on Based on template positions steps gel purification)amount rCTP amount rGTP amount rUTP amount amount ¹G-¹³U 2 36.9%/23%6.7% 36.9% 4.9% 29.5% 60% ⁵¹U 5 32.0%/18% 5.8% 32.0% 4.2% 25.6% 81%²⁰A-²⁶G 6 30.3%/22% 5.5% 30.3% 4.0% 24.2% 82% ⁴⁸C-⁵⁴A 9  10.2%/5.3% 1.9%10.2% 1.3% 8.2% 78% ²¹A, ³⁸C, 9  12.2%/6.9% 2.2% 12.2% 1.6% 9.8% 79%³⁹G, ⁶⁰U ³⁴G-⁴²C 10  17.6%/12.5% 3.2% 17.6% 2.3% 14.1% 84% ²⁰A-²⁶G, 12 8.5%/5.0% 1.5% 8.5% 1.1% 6.8% 82% ⁴⁸C-⁵⁴A None or all^(a) 1 13.3(DNA-bead 11.4% 7.3% 7.9% 13.6% 13.3 used) None or all^(b) 1 756 (freeDNA 28.7% 18.7% 20.1% 34.5% 756 template used) Note: ^(a)Use beadattached DNA as template. The 71-nt RNA is transcribed in a multiplecycles of one-step transcription reaction. ^(b)Use free DNA (not beadattached) as template as in traditional liquid phase transcription andthe 71-nt RNA was transcribed in a multiple cycles of one-steptranscription reaction.

Example 2 Selective Labeling of RNA Segments

FIGS. 7-13 show examples of selectively labeled RNAs that weresynthesized according to the method disclosed herein. The RNAs containsegments labeled with ¹³C/¹⁵N nucleotides. The RNAs were detected usingHSQC 2D NMR, which confirm that portions of the RNAs were selectivelylabeled.

Example 3 Method and Apparatus for Selectively Labeling RNA Segments

The example illustrates a RNA synthesis reaction for selectivelylabeling RNA segments, and an apparatus/automated platform for carryingout the method. FIG. 15 shows the initiation, elongation, andtermination steps of the RNA synthesis reaction. FIG. 16 shows thelayout of a deck of a robotic liquid handling platform for carrying outautomated RNA synthesis, and FIGS. 17 and 18 shows further views of theautomated platform. Buffers labeled 1, 2 and 4 are kept in 20 mL or 40mL vials in racks of 2×4 (on left side of deck). Temperature control maynot be needed. Buffers labeled 3 and 5 are kept in larger reservoirskept off the deck with dedicated probes for their use only. Notemperature control may be needed, and keeping dedicated probeseliminates any cross contamination. Reactants 6-13 (on right side ofdeck) are kept in 20 mL or 40 L vials in a rack of 2×4 and kept at 4° C.The deck in FIG. 15 has a heating vortexer mixing, but the vortexer canbe replaced with a “tumbling” module for mixing. The tumbling modulecould rotate reactions 360° without creating bubbles. The deck maycontain extra adaptors for parking extra buffers and/or filtrationcartridges. Component 14 is a rack of 7 mL reactors/filtrationcartridges, and component 15 is multiple racks for 40 mL collectionvials, which are kept at 4° C.

The apparatus includes an instrument gripper that allows for thetransportation of labware and assembly and disassembly of a filtrationstation automatically. The apparatus also includes an arm (“ARM 1”), a6-way valve, syringe pumps, and solid phase extraction (SPE) components,including a SPE spot park, SPE vacuum lid, and SPE vacuum station. Theapparatus also uses positive pressure, which can be regulated, withreactor/filtration vessels. The apparatus can also maintain samplesunder inert conditions using multi-channel probes that allow fordispensing of liquids and inert gas. The apparatus can accept input andexport files for an internal laboratory information management system,which instruct the apparatus to perform the tasks for synthesizing RNA.

The apparatus carries out the synthesis reaction in FIG. 15 as follows.For block 1 (green block), (a) a bead suspension is provided in 6, 5 mLreactor/filtration vessels in a rack. The rack is temperature controlledon gentle vortexing or tumbling at 37° C. (b) The apparatus then adds acombination of buffers and reactants (buffer-1, buffer-2, andbuffers/reactants 6-13) to the suspension defined by an input file. (c)The reaction is gently vortexed/tumbled at 37° C. for 15 minutes. (d)The apparatus then moves the rack of reaction vials to a temperaturecontrolled position on the deck at 4° C. for 30 minutes. (e) The rack ofreaction/filtration vessels is then moved to a filtration system atambient temperature. (f) A buffer (buffer-5) is added by the apparatus,and (g) the reaction is gently mixed/tumbled. (h) The reactions arefiltered to separate the solid phase from the liquid phase, and thefiltrant goes to waste. (i) Steps (f)-(h) are repeated X (X=3-6) times,according to the input file.

For block 2 (cyan block), a rack of reaction vials is placed on aposition on the deck at ambient temperature (25° C.). (a) The apparatusadds a combination of buffers and reactants (from buffer/reactants 1-13,as desired) according to the input file. (b) The reaction is incubatedat ambient temperature for 10 minutes and gently vortexed/tumbled. (c)The reactor/filtration vessels are moved to the filtration station onthe deck, which will be at ambient temperature. (d) The apparatus addsbuffer-5 to the reaction vessels, and (e) gently mixes/tumbles thereaction. (f) The reaction is filtered to separate the solid and liquidphases, and the filtrant goes to waste. Steps (d)-(f) are repeated Y(Y=3-6) times according to the input file. Steps (a)-(g) are repeated Ntimes according to the input file.

For block 3 (red block), reaction vessels are at ambient temperature.(a) The apparatus adds a combination of buffers and reactants (frombuffers/reactants 1-13, as desired) according to the input file. (b) Thereactions are incubated at ambient temperature for 15 minutes and gentlyvortexed/tumbled. (c) A collection of vials are sitting on 4° C.temperature controlled positions. While the reactions are incubating,the collection vials are moved from the 4° C. positions on the deck intoposition at the filtration station, which is at ambient temperature. (d)The apparatus moves the reactor/filtration vessels to the filtrationstation on the deck, which will be at ambient temperature. (e) Thereactions are filtered at ambient temperature to separate the solid andliquid phases, and the solid phase is collected into the collectionvials. (f) The collection vials are moved back to position on the deckto be kept at 4° C.

1. A method for synthesizing a RNA, comprising performing an initiationstage, an elongation stage, and a termination stage, wherein: (a) theinitiation stage comprises: (i) providing a solid phase comprising a DNAtemplate, wherein the DNA is attached to a solid substrate; (ii)providing a first liquid phase comprising a RNA polymerase andribonucleoside triphosphates (rNTPs); (iii) mixing the solid phase andfirst liquid phase; (iv) incubating the solid phase and first liquidphase at 4-37° C. for at least 10 minutes to initiate synthesis of theRNA; (v) pausing the RNA synthesis by incubating the solid phase andfirst liquid phase at 0-5° C. for at least 10 minutes, whereupon thesolid phase comprises the RNA polymerase and the RNA being synthesized;and (vi) separating the solid phase from the first liquid phase; (b) theelongation stage comprises: (i) providing a second liquid phasecomprising rNTPs; (ii) mixing the solid phase and second liquid phase;(iii) incubating the solid phase and second liquid phase at 4-37° C. forat least 10 minutes to elongate the RNA; (iv) pausing the RNA synthesisby incubating the solid phase and second liquid phase at 0-5° C. for atleast 10 minutes; (v) separating the solid phase from the second liquidphase; and (vi) repeating steps (i)-(v) of part (b) n times, wherein nis equal to 1-100, and wherein the rNTPs in the second liquid phase arethe same or different in each repeat; (c) the termination stagecomprises: (i) providing a third liquid phase comprising rNTPs; (ii)mixing the solid phase with the third liquid phase; (iii) incubating thesolid phase and third liquid phase at 4-37° C. for at least 10 minutes;and (iv) pausing the RNA synthesis by incubating the solid phase andthird liquid phase at 0° C. for at least 10 minutes; wherein steps(a)-(c) are repeated m times, wherein m is equal to 1-100, and whereinrNTPs of at least one of the first liquid phase, the second liquidphase, or third liquid phase comprise a label.
 2. The method of claim 1,wherein the DNA has a density of 30-80% on the solid substrate.
 3. Themethod of claim 1, wherein the solid substrate is a bead comprising agel, glass, or a synthetic polymer.
 4. The method of claim 3, whereinthe bead has a diameter of 5-100 μm.
 5. The method of claim 1, whereinthe concentration of DNA is 30 μm-1 nM.
 6. The method of claim 5,wherein the concentration of rNTPs is 1-100 times the DNA concentration.7. The method of claim 1, wherein the RNA polymerase is T7 RNApolymerase.
 8. The method of claim 1, wherein the label is selected fromthe group consisting of ¹³C/¹⁵N, ²H, Cy3, Cy5, a fluorophore, a heavyatom, and a chemical modification.